Transcriptomic analysis of the phytopathogenic oomycete Phytophthora cactorum provides insights into infection-related effectors

Chen, Xiao-Ren; Zhang, Bo-Yue; Xing, Yu-Ping; Li, Qi-Yuan; Li, Yan-Peng; Tong, Yun-Hui; Xu, Jing-You

doi:10.1186/1471-2164-15-980

Table 4 Canonical and variant RXLR-dEER motifs and the WY-domain found in P. cactorum transcriptome protein models

From: Transcriptomic analysis of the phytopathogenic oomycete Phytophthora cactorum provides insights into infection-related effectors

Effector name	Transcriptome unigene ID^a	Protein length	SignalP HMM probability^b	SignalP NN mean S score^b	SignalP length^b	RXLR start	RXLR motif^c	dEER start	dEER motif^cd	Stop codon	Evidence^e	WY-domain^cf	Seq-from^f	Seq-to^f	E-value^f	Score^f
PcRXLR1	467	180	0.999	0.950	20	50	RYLR	62	DEER	181	MB	—	—	—	—	—
PcRXLR2	3444	276	0.999	0.863	23	51	RSLR	63	NENEER	277	MB	2/2	218	261	4.50e-06	13
PcRXLR3	4585	160	0.997	0.907	20	51	RFLR	86	DEER	161	MBPR	1/1	94	141	2.90e-11	29.6
PcRXLR4	4911	198	0.999	0.918	18	57	RLLR	71	DDEEER	199	MBR	2/2	138	177	1.70e-06	14.3
PcRXLR5	7413	288	0.998	0.955	22	42	RSLR	56	EDNEER	289	MBPR	1/3	106	125	0.00015	8.1
PcRXLR6	12534	260	1.000	0.848	20	50	RFLR	68	EER	261	MBPR	—	—	—	—	—
PcRXLR7	14177	253	0.998	0.913	16	95	RLLR	114	EER	254	MBPR	—	—	—	—	—
PcRXLR8	14674	147	0.995	0.892	25	48	RFLR	66	DDEER	148	MBPR	2/3	89	112	0.00026	7.4
PcRXLR9	14719	132	1.000	0.885	23	41	RSLR	50	EER	133	MBPR	1/1	66	114	9.70e-07	15.1
PcRXLR10	15159	136	0.998	0.818	23	56	RLLR	71	EEEER	137	MBP	2/2	77	125	4.90e-11	28.8
PcRXLR11	15234	171	1.000	0.959	21	54	RFLR	74	EER	172	MBPR	—	—	—	—	—
PcRXLR12	15411	333	1.000	0.898	24	29	RGLR	41	EDDE	334	MB	—	—	—	—	—
PcRXLR13	15681	407	1.000	0.944	20	52	RFLR	66	EER	408	MBPR	3/4	270	317	4.60e-17	48.1
PcRXLR14	16067	358	0.999	0.866	19	49	RFLR	65	EEK	359	MBP	2/3	178	222	1.60e-06	14.4
PcRXLR15	17198	503	1.000	0.940	19	52	RFLR	58	DDEER	504	MBP	4/5	355	402	5.20e-20	57.5
PcRXLR16	17759	162	1.000	0.877	24	30	RRLR	75	DEQ	163	MBPR	—	—	—	—	—
PcRXLR17	17849	349	0.998	0.853	20	42	RSLR	52	EDDEER	350	MBPR	1/4	105	153	2.10e-20	58.7
PcRXLR18	17862	244	0.985	0.698	23	55	RFLR	69	EDDEER	245	MB	1/1	180	219	7.80e-11	28.2
PcRXLR19	17955	134	1.000	0.967	20	48	RFLR	62	DEER	135	MB	1/1	77	120	7.70e-08	18.6
PcRXLR20	18066	171	1.000	0.927	23	58	RLLR	80	EER	172	MBPR	—	—	—	—	—
PcRXLR21	18476	142	1.000	0.927	21	50	RSLR	62	DEEEDEEDEER	143	MBPR	—	—	—	—	—
PcRXLR22	18992	290	1.000	0.907	21	56	RFLR	62	DDEER	291	MBPR	2/3	155	199	5.30e-08	19.2
PcRXLR23	19550	116	0.999	0.887	21	48	RHLR	65	DEER	117	MBPR	—	—	—	—	—
PcRXLR24	19979	309	1.000	0.831	24	36	RLLR	45	DEE	310	MB	1/3	69	117	3.70e-18	51.5
PcRXLR25	20127	145	0.998	0.798	20	54	RFLR	74	EER	146	MBPR	—	—	—	—	—
PcRXLR26	20211	233	0.999	0.926	21	42	RALR	55	EER	234	MB	1/2	90	125	1.70e-10	27.1
PcRXLR27	20751	133	0.999	0.862	22	52	RFLR	63	DEER	134	MBPR	—	—	—	—	—
PcRXLR28	3199	60	0.999	0.910	24	38	RFLR	—	—	61	MB	—	—	—	—	—
PcRXLR29	13894	330	0.983	0.620	25	47	RSLR	—	—	331	MB	—	—	—	—	—
PcRXLR30	18832	148	0.975	0.929	25	46	RFLR	—	—	149	MBP	1/1	76	124	4.20e-14	38.6
PcRXLR31	20872	211	0.999	0.950	19	73	RKLR	—	—	212	MB	—	—	—	—	—
PcRXLR32	1468	120	0.999	0.796	20	43	RYLK	58	DEDR	121	MB	—	—	—	—	—
PcRXLR33	1929	143	0.999	0.875	22	46	RFLT	55	DDER	144	MB	1/1	70	118	2.50e-19	55.3
PcRXLR34	2443	185	1.000	0.958	20	42	RNLK	58	DEER	186	MB	—	—	—	—	—
PcRXLR35	4402	157	1.000	0.948	23	41	RVLL	53	EER	158	MB	2/3	90	121	4.90e-05	9.7
PcRXLR36	7520	210	1.000	0.845	25	36	RLLS	52	ER	211	MB	—	—	—	—	—
PcRXLR37	14168	143	0.998	0.890	24	43	RKLA	59	EER	144	MB	—	—	—	—	—
PcRXLR38	17882	139	0.999	0.845	23	53	RMLK	64	DDEER	140	MB	1/1	86	132	1.40e-07	17.8
PcRXLR39	19735	171	0.933	0.768	23	42	RSLK	58	DEDR	172	MB	—	—	—	—	—
PcRXLR40	20420	190	0.996	0.924	21	42	RHLK	56	EER	191	MB	—	—	—	—	—
PcRXLR41	1130	—	1.000	0.953	20	52	RLLR	65	EER	—	MB	1/2	91	137	5.50e-20	57.4
PcRXLR42	6874	—	1.000	0.926	20	40	RSLR	52	DDEEER	—	MB	—	—	—	—	—
PcRXLR43	11787	—	1.000	0.817	23	42	RHLR	55	EE	—	MB	—	—	—	—	—
PcRXLR44	13785	—	1.000	0.882	22	46	RFLR	55	DEER	—	MB	—	—	—	—	—
PcRXLR45	16936	—	0.995	0.856	24	35	RMLR	46	EEE	—	MB	—	—	—	—	—
PcRXLR46	3185	—	—	—	—	15	RLLW	36	EDDEEER	—	MB	1/2	57	104	2.60e-08	20.1
PcRXLR47	3331	—	—	—	—	16	RSLR	31	EER	—	MB	—	—	—	—	—
PcRXLR48	6076	—	—	—	—	53	RLLR	63	EE	—	MB	—	—	—	—	—
PcRXLR49	8191	—	—	—	—	20	RYLR	30	EDEDR	—	MB	—	—	—	—	—
PcRXLR50	8328	—	—	—	—	36	RRLR	52	EER	—	MB	1/1	66	114	8.30e-15	40.9
PcRXLR51	8440	—	—	—	—	21	RYLR	39	DEER	—	MB	1/1	101	142	1.20e-06	14.8
PcRXLR52	11059	—	—	—	—	18	RLLR	28	EN	—	MB	—	—	—	—	—
PcRXLR53	11691	—	—	—	—	29	RSLR	39	DEER	—	MB	1/1	46	74	6.00e-08	19
PcRXLR54	12599	—	—	—	—	28	RYLR	44	EER	—	MB	—	—	—	—	—
PcRXLR55	1675	—	—	—	—	—	—	3	EER	—	MB	—	—	—	—	—
PcRXLR56	6278	—	—	—	—	—	—	11	EER	—	MB	1/1	35	66	9.50e-06	12
PcRXLR57	10850	—	—	—	—	—	—	1	DDE	—	MB	2/3	120	167	4.40e-16	44.9
PcRXLR58	1999	—	—	—	—	—	—	3	DEER	265	MB	3/4	141	189	1.90e-13	36.5
PcRXLR59	18301	—	—	—	—	—	—	18	DDDEER	440	MB	4/5	305	353	2.50e-11	29.8
PcRXLR60	20091	—	—	—	—	—	—	1	EDEER	314	MB	—	—	—	—	—
PcRXLR61	21078	—	—	—	—	18	RGLR	28	ND	307	MB	—	—	—	—	—
PcRXLR62	17023	160	0.986	0.409	25	54	RFLR	65	DNEER	161	MB	—	—	—	—	—
PcRXLR63	17457	134	0.999	0.925	19	37	GILR	51	EEER	135	MB	—	—	—	—	—
PcRXLR64	13871	117	0.996	0.772	21	45	KLLR	61	EQEER	118	MB	—	—	—	—	—

^aEffectors were predicted from the unigene sequences.
^bHidden Markov model (HMM) probability, NN mean S score, and signal peptide length were predicted using SignalP v3.0.
^cAll sequence coordinates are given in amino acid residues.
^dDetermined as two or more D,E,N and/or Q residues followed by a R or K residue: [DENQ]{2,}[RK].
^eEvidence codes for RXLR gene prediction: M (motif search), B (BLAST comparison), P (PCR validation), and R (RT-PCR).
^fWY-domain was predicted using the HMM for the WY-domain as described in [38] with the HMM score cut-off of 0.0. The “—” means that no WY-domain was predicted.

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ISSN: 1471-2164

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